What’s new¶
0.5.4 (20th of July 2017)¶
- [DOC] Improved report summaries describing steps taken (#584)
- [ENH] Uniformize command-line argument style (#592)
0.5.3 (18th of July 2017)¶
With thanks to Yaroslav Halchenko for contributions.
- [ENH] High-pass filter time series prior to CompCor (#577)
- [ENH] Validate and minimally conform BOLD images (#581)
- [FIX] Bug that prevented PE direction estimation (#586)
- [DOC] Log version/time in report (#587)
0.5.2 (30th of June 2017)¶
With thanks to James Kent for contributions.
- [ENH] Calculate noise components in functional data with ICA-AROMA (#539)
- [FIX] Remove unused parameters from function node, resolving crash (#576)
0.5.1 (24th of June 2017)¶
- [FIX] Invalid parameter in
bbreg_wf
(#572)
0.5.0 (21st of June 2017)¶
With thanks to James Kent for contributions.
- [ENH] EXPERIMENTAL: Fieldmap-less susceptibility correction with
--use-syn-sdc
option (#544) - [FIX] Reduce interpolation artifacts in ConformSeries (#564)
- [FIX] Improve consistency of handling of fieldmaps (#565)
- [FIX] Apply T2w pial surface refinement at correct stage of FreeSurfer pipeline (#568)
- [ENH] Add
--anat-only
workflow option (#560) - [FIX] Output all tissue class/probability maps (#569)
- [ENH] Upgrade to ANTs 2.2.0 (#561)
0.4.6 (14th of June 2017)¶
- [ENH] Conform and minimally resample multiple T1w images (#545)
- [FIX] Return non-zero exit code on all errors (#554)
- [ENH] Improve error reporting for missing subjects (#558)
0.4.5 (12th of June 2017)¶
With thanks to Marcel Falkiewicz for contributions.
- [FIX] Correctly display help in
fmriprep-docker
(#533) - [FIX] Avoid invalid symlinks when running FreeSurfer (#536)
- [ENH] Improve dependency management for users unable to use Docker/Singularity containers (#549)
- [FIX] Return correct exit code when a Function node fails (#554)
0.4.4 (20th of May 2017)¶
With thanks to Feilong Ma for contributions.
- [ENH] Option to provide a custom reference grid image (
--output-grid-reference
) for determining the field of view and resolution of output images (#480) - [ENH] Improved EPI skull stripping and tissue contrast enhancements (#519)
- [ENH] Improve resource use estimates in FreeSurfer workflow (#506)
- [ENH] Moved missing values in the DVARS* and FramewiseDisplacement columns of the _confounds.tsv from last row to the first row (#523)
- [ENH] More robust initialization of the normalization procedure (#529)
0.4.3 (10th of May 2017)¶
- [ENH]
--output-space template
targets template specified by--template
flag (MNI152NLin2009cAsym
supported) (#498) - [FIX] Fix a bug causing small numerical discrepancies in input data voxel size to lead to different FOV of the output files (#513)
0.4.2 (3rd of May 2017)¶
- [ENH] Use robust template generation for multiple T1w images (#481)
- [ENH] Anatomical MNI outputs respect
--output-space
selection (#490) - [ENH] Added support for distortion correction using opposite phase encoding direction EPI images (#493)
- [ENH] Switched to FSL BET for skullstripping of EPI images (#493)
- [ENH]
--omp-nthreads
controls maximum per-process thread count; replaces--ants-nthreads
(#500)
0.4.1 (20th of April 2017)¶
- Hotfix release (dependencies and deployment system)
0.4.0 (20th of April 2017)¶
- [ENH] Added an option to choose the degrees of freedom used when doing BOLD to T1w coregistration (
--bold2t1w_dof
). Set default to 9 to account for field inhomogeneities and coils heating up (#448) - [ENH] Added support for phase difference and GE style fieldmaps (#448)
- [ENH] Generate GrayWhite, Pial, MidThickness and inflated surfaces (#398)
- [ENH] Memory and performance improvements for calculating the EPI reference (#436)
- [ENH] Sample functional series to subject and
fsaverage
surfaces (#391) - [ENH] Output spaces for functional data may be selected with
--output-space
option (#447) - [DEP]
--skip-native
functionality replaced by--output-space
(#447) - [ENH]
fmriprep-docker
wrapper script simplifies running in a Docker environment (#317)
0.3.2 (7th of April 2017)¶
With thanks to Asier Erramuzpe for contributions.
- [ENH] Added optional slice time correction (#415)
- [ENH] Removed redundant motion parameter conversion step using avscale (#415)
- [ENH] FreeSurfer submillimeter reconstruction may be disabled with
--no-submm-recon
(#422) - [ENH] Switch bbregister init from
fsl
tocoreg
(FreeSurfer native #423) - [ENH] Motion estimation now uses a smart reference image that takes advantage of T1 saturation (#421)
- [FIX] Fix report generation with
--reports-only
(#427)
0.3.1 (24th of March 2017)¶
- [ENH] Perform bias field correction of EPI images prior to coregistration (#409)
- [FIX] Fix an orientation issue affecting some datasets when bbregister was used (#408)
- [ENH] Minor improvements to the reports aesthetics (#428)
0.3.0 (20th of March 2017)¶
- [FIX] Affine and warp MNI transforms are now applied in the correct order
- [ENH] Added preliminary support for reconstruction of cortical surfaces using FreeSurfer
- [ENH] Switched to bbregister for BOLD to T1 coregistration
- [ENH] Switched to sinc interpolation of preprocessed BOLD and T1w outputs
- [ENH] Preprocessed BOLD volumes are now saved in the T1w space instead of mean BOLD
- [FIX] Fixed a bug with MCFLIRT interpolation inducing slow drift
- [ENH] All files are now saved in Float32 instead of Float64 to save space
0.2.0 (13th of January 2017)¶
- Initial public release
0.1.2 (3rd of October 2016)¶
- [FIX] Downloads from OSF, remove data downloader (now in niworkflows)
- [FIX] pybids was missing in the install_requires
- [DEP] Deprecated -S/–subject-id tag
- [ENH] Accept subjects with several T1w images (#114)
- [ENH] Documentation updates (#130, #131)
- [TST] Re-enabled CircleCI tests on one subject from ds054 of OpenfMRI
- [ENH] Add C3D to docker image, updated poldracklab hub (#128, #119)
- [ENH] CLI is now BIDS-Apps compliant (#123)
0.1.1 (30th of July 2016)¶
- [ENH] Grabbit integration (#113)
- [ENH] More outputs in MNI space (#99)
- [ENH] Implementation of phase-difference fieldmap estimation (#91)
- [ENH] Fixed bug using non-RAS EPI
- [ENH] Works on ds005 (datasets without fieldmap nor sbref)
- [ENH] Outputs start to follow BIDS-derivatives (WIP)
0.0.1¶
- [ENH] Added Docker images
- [DOC] Added base code for automatic publication to RTD.
- Set up CircleCI with a first smoke test on one subject.
- BIDS tree scrubbing and subject-session-run selection.
- Refactored big workflow into consistent pieces.
- Migrated Craig’s original code